Title: Prepare Species Distributions for the Use in Phylogenetic
Analyses
Description: Preparation of species occurrences and distribution data for the use in phylogenetic analyses. SpeciesgeocodeR is built for data cleaning, data exploration and data analysis and especially suited for biogeographical and ecological questions on large datasets. The package includes the easy creation of summary-tables and -graphs and geographical maps, the automatic cleaning of geographic occurrence data, the calculating of coexistence matrices and species ranges (EOO) as well as mapping diversity in geographic areas.
Author: Alexander Zizka [aut, cre]
Maintainer: Alexander Zizka <alexander.zizka@bioenv.gu.se>
Diff between speciesgeocodeR versions 1.0-3 dated 2015-07-14 and 1.0-4 dated 2015-10-17
speciesgeocodeR-1.0-3/speciesgeocodeR/inst/doc/data_cleaning_and_exploration.Rmd |only speciesgeocodeR-1.0-3/speciesgeocodeR/inst/doc/data_cleaning_and_exploration.html |only speciesgeocodeR-1.0-4/speciesgeocodeR/DESCRIPTION | 15 - speciesgeocodeR-1.0-4/speciesgeocodeR/MD5 | 70 +++--- speciesgeocodeR-1.0-4/speciesgeocodeR/NAMESPACE | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/R/GeoClean.R | 35 ++- speciesgeocodeR-1.0-4/speciesgeocodeR/R/ReadPoints.R | 80 +++++-- speciesgeocodeR-1.0-4/speciesgeocodeR/R/SpGeoCod.R | 8 speciesgeocodeR-1.0-4/speciesgeocodeR/R/SpGeoCodH.R | 4 speciesgeocodeR-1.0-4/speciesgeocodeR/R/SpeciesGeoCoder.R | 38 +-- speciesgeocodeR-1.0-4/speciesgeocodeR/R/Spgc2BioGeoBEARS.R |only speciesgeocodeR-1.0-4/speciesgeocodeR/R/WriteOut.R | 62 +++-- speciesgeocodeR-1.0-4/speciesgeocodeR/R/speciesgeocodeR-internal.R | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/inst/doc/data_cleaning_and_exploration.pdf |binary speciesgeocodeR-1.0-4/speciesgeocodeR/man/CoExClass.Rd | 62 ++--- speciesgeocodeR-1.0-4/speciesgeocodeR/man/GeoClean.Rd | 43 +-- speciesgeocodeR-1.0-4/speciesgeocodeR/man/GetElevation.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/MapGrid.Rd | 74 +++--- speciesgeocodeR-1.0-4/speciesgeocodeR/man/MapRichness.Rd | 112 +++++----- speciesgeocodeR-1.0-4/speciesgeocodeR/man/PlotHull.Rd | 4 speciesgeocodeR-1.0-4/speciesgeocodeR/man/ReadPoints.Rd | 18 + speciesgeocodeR-1.0-4/speciesgeocodeR/man/RichnessGrid.Rd | 3 speciesgeocodeR-1.0-4/speciesgeocodeR/man/SpGeoCod.Rd | 21 + speciesgeocodeR-1.0-4/speciesgeocodeR/man/SpGeoCodH.Rd | 23 -- speciesgeocodeR-1.0-4/speciesgeocodeR/man/SpeciesGeoCoder.Rd | 23 +- speciesgeocodeR-1.0-4/speciesgeocodeR/man/Spgc2Biogeobears.Rd |only speciesgeocodeR-1.0-4/speciesgeocodeR/man/WriteOut.Rd | 11 speciesgeocodeR-1.0-4/speciesgeocodeR/man/WwfLoad.Rd | 71 +++--- speciesgeocodeR-1.0-4/speciesgeocodeR/man/countryref.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/lemurs.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/lemurs_in.Rd | 6 speciesgeocodeR-1.0-4/speciesgeocodeR/man/lemurs_test.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/mdg_biomes.Rd | 6 speciesgeocodeR-1.0-4/speciesgeocodeR/man/mdg_poly.Rd | 8 speciesgeocodeR-1.0-4/speciesgeocodeR/man/plot.spgeoOUT.Rd | 8 speciesgeocodeR-1.0-4/speciesgeocodeR/man/speciesgeocodeR-package.Rd | 99 ++++---- speciesgeocodeR-1.0-4/speciesgeocodeR/man/summary.spgeoIN.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/summary.spgeoOUT.Rd | 6 38 files changed, 504 insertions(+), 420 deletions(-)
More information about speciesgeocodeR at CRAN
Permanent link
Title: Diverse Basic Statistical and Graphical Functions
Diff between RVAideMemoire versions 0.9-50 dated 2015-08-08 and 0.9-51 dated 2015-10-17
Description: Contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Hervé
Maintainer: Maxime Hervé
DESCRIPTION | 8 -
MD5 | 22 ++--
NEWS | 7 +
R/MVA.biplot.R | 56 +++++++++--
R/MVA.load.R | 2
R/MVA.scores.R | 2
R/byf.hist.R | 16 +--
R/plotresid.R | 215 +++++++++++++++++++++++--------------------
R/zzz.R | 2
man/RVAideMemoire-package.Rd | 4
man/byf.hist.Rd | 8 +
man/plotresid.Rd | 8 -
12 files changed, 212 insertions(+), 138 deletions(-)
Title: Discrete Weibull Distributions (Type 1 and 3)
Description: Probability mass function, distribution function, quantile function, random generation and parameter estimation for the type I and III discrete Weibull distributions.
Author: Alessandro Barbiero
Maintainer: Alessandro Barbiero <alessandro.barbiero@unimi.it>
Diff between DiscreteWeibull versions 1.0.1 dated 2015-07-08 and 1.1 dated 2015-10-17
DESCRIPTION | 8 +-- MD5 | 28 ++++++------- R/Edweibull.R | 75 ++++++++++++++++++++++-------------- man/DiscreteWeibull-package.Rd | 9 ++-- man/Edweibull.Rd | 19 ++++++--- man/Edweibull3.Rd | 40 +++++++++---------- man/ddweibull.Rd | 22 +++++----- man/ddweibull3.Rd | 84 ++++++++++++++++++++--------------------- man/estdweibull.Rd | 23 +++++------ man/estdweibull3.Rd | 72 +++++++++++++++++------------------ man/loglikedw.Rd | 10 ++-- man/loglikedw3.Rd | 12 ++--- man/lossdw.Rd | 8 +-- man/lossdw3.Rd | 12 ++--- man/varFisher.Rd | 7 +-- 15 files changed, 228 insertions(+), 201 deletions(-)
More information about DiscreteWeibull at CRAN
Permanent link
Title: Toolkit for Item Factor Analysis with OpenMx
Description: Tools, tutorials, and demos of Item Factor Analysis using OpenMx.
Author: Joshua N. Pritikin [cre, aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between ifaTools versions 0.6 dated 2015-07-21 and 0.8 dated 2015-10-17
DESCRIPTION | 14 +++++++------- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 2 +- R/model.R | 17 +++++++---------- R/plot.R | 4 +++- inst/itemModelExplorer/server.R | 16 +++++++++++++++- inst/itemModelExplorer/ui.R | 3 ++- inst/modelBuilder/www/sort.css | 2 ++ man/SitemPlot.Rd | 3 ++- man/addExploratoryFactors.Rd | 3 ++- man/iccPlot.Rd | 3 ++- man/itemModelExplorer.Rd | 3 ++- man/itemResponseMap.Rd | 7 ++++++- man/modelBuilder.Rd | 3 ++- man/plotInformation.Rd | 3 ++- man/replicateModelBy.Rd | 3 ++- man/uniquenessPrior.Rd | 3 ++- man/univariatePrior.Rd | 3 ++- 18 files changed, 78 insertions(+), 48 deletions(-)
Title: Creates a Model Matrix via Feature Hashing with a Formula
Interface
Description: Feature hashing, also called as the hashing trick, is a method to transform
features of a instance to a vector. Thus, it is a method to transform a real dataset to a matrix.
Without looking up the indices in an associative array,
it applies a hash function to the features and uses their hash values as indices directly.
The method of feature hashing in this package was proposed in Weinberger et al. (2009).
The hashing algorithm is the murmurhash3 from the digest package.
Please see the README in https://github.com/wush978/FeatureHashing for more information.
Author: Wush Wu [aut, cre],
Michael Benesty [aut, ctb]
Maintainer: Wush Wu <wush978@gmail.com>
Diff between FeatureHashing versions 0.9.1 dated 2015-09-22 and 0.9.1.1 dated 2015-10-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/doc/FeatureHashing.html | 4 ++-- src/hash_function.h | 1 + src/hash_internal.cpp | 3 ++- tests/test-progress_bar.R | 4 ++-- 6 files changed, 15 insertions(+), 13 deletions(-)
More information about FeatureHashing at CRAN
Permanent link
Title: AMCE Estimator for Conjoint Experiments
Description: An R implementation of the Average Marginal Component-specific Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and Yamamoto T. (2014) Causal Inference in Conjoint Analysis: Understanding Multi-Dimensional Choices via Stated Preference Experiments. Political Analysis 22(1):1-30.
Author: Anton Strezhnev, Elissa Berwick, Jens Hainmueller, Daniel Hopkins, Teppei Yamamoto
Maintainer: Anton Strezhnev <astrezhnev@fas.harvard.edu>
Diff between cjoint versions 2.0.0 dated 2015-07-24 and 2.0.1 dated 2015-10-17
DESCRIPTION | 8 MD5 | 8 NAMESPACE | 1 R/cjoint.R | 889 +++++++++++++++++++++++++++++++++++++------------------ man/plot.amce.Rd | 6 5 files changed, 625 insertions(+), 287 deletions(-)
Title: Search and Download Papers from the bioRxiv Preprint Server
Description: The bioRxiv preprint server (http://www.biorxiv.org) is a website where scientists can post preprints of scholarly texts in biology. Users can search and download PDFs in bulk from the preprint server. The text of abstracts are stored as raw text within R, and PDFs can easily be saved and imported for text mining with packages such as 'tm'.
Author: Edmund Hart [aut, cre]
Maintainer: Edmund Hart <edmund.m.hart@gmail.com>
Diff between biorxivr versions 0.1.1 dated 2015-05-28 and 0.1.2 dated 2015-10-17
DESCRIPTION | 8 +-- MD5 | 32 ++++++------ NAMESPACE | 6 +- R/bx_download.R | 1 R/bx_extract.R | 1 R/bx_search.R | 1 inst/doc/vignette.R | 3 + inst/doc/vignette.Rmd | 4 + inst/doc/vignette.html | 94 ++++++++++++++++++------------------ man/bx_download.Rd | 2 man/bx_extract.Rd | 2 man/bx_extract_single.Rd | 2 man/bx_search.Rd | 2 man/plot.biorxiv_paper.Rd | 2 man/print.summary.biorxiv_search.Rd | 2 man/summary.biorxiv_search.Rd | 2 vignettes/vignette.Rmd | 4 + 17 files changed, 95 insertions(+), 73 deletions(-)
Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts versions 0.3.2 dated 2015-09-03 and 0.4.1 dated 2015-10-17
DESCRIPTION | 11 +-- MD5 | 19 +++-- NAMESPACE | 7 +- NEWS | 12 +++ R/qic.R | 196 +++++++++++++++++++++++++++++++++++++++++--------------- R/tcc.R |only R/trc.R | 54 ++++++++++----- README.md | 3 man/plot.tcc.Rd |only man/qic.Rd | 26 ++++--- man/tcc.Rd |only man/trc.Rd | 7 +- 12 files changed, 240 insertions(+), 95 deletions(-)
Title: Diagnostics Plots for Bicluster Data
Description: Diagnostic tools based on two-way
anova and median-polish residual plots for Bicluster output
obtained from packages; "biclust" by Kaiser et al.(2008),"isa2"
by Csardi et al. (2010) and "fabia" by Hochreiter et al.
(2010). Moreover, It provides visualization tools for bicluster
output and corresponding non-bicluster rows- or columns
outcomes. It has also extended the idea of Kaiser et al.(2008)
which is, extracting bicluster output in a text format, by
adding two bicluster methods from the fabia and isa2 R
packages.
Author: Aregay Mengsteab, Martin Otava, Tatsiana Khamiakova, Ewoud De Troyer
Maintainer: Ewoud De Troyer <ewoud.detroyer@uhasselt.be>
Diff between BcDiag versions 1.0.9 dated 2015-10-10 and 1.0.10 dated 2015-10-17
DESCRIPTION | 12 +-- MD5 | 6 - R/profileBic.R | 209 ++++++++++++++++++++++++++++++++++++++++++++++-------- man/profileBic.Rd | 5 + 4 files changed, 192 insertions(+), 40 deletions(-)